Exam 1: Biochem Flashcards
Compare the predominating interactions of the different amino acid R groups
Nonpolar aliphatic and aromatic R groups: Van der Waal’s interactions; hydrophobic and associate with the interior of amino acids
Sulfur-containing R groups: can form disulfide bonds
Polar, uncharged R groups: Hydrogen binding
Charged R groups: electrostatic interactions
When pKa of an ionizable group equals the pH in its environment, which form dominates?
HA and A- exist in equilibrium.
When the pH of an environment is more basic than the pKa of an ionizable group, which form of that group dominates?
The A- form.
When the pH of an environment is more acidic than the pKa of an ionizable group, which form dominates?
The HA form.
What is the pKa of carboxylic acid?
Between 2-4
What is the pKa of an amine group?
Approximately 9.
Describe endocrine signaling.
In endocrine signaling, ligands travel relatively long distances via the bloodstream. The ligand may be hormones (small molecules or proteins secreted by glands) or cytokines (small proteins secreted by non-glands, usually have immunomodulating function).
Describe autocrine signaling.
A cell releases a signal and responds to the ligand itself. This is important in tissue growth, organ development, immune response and inflammatory response.
Describe paracrine signaling.
A cell releases a signal that travels a short distance to its neighbor. Think synaptic signaling.
A cell secretes a ligand and the downstream effect is that 1,000s of proteins are modified. This is an example of what important quality of cell signal transduction?
Amplification.
Hormone X with a really intimidating name binds with endohoohahlongname receptor and triggers a bunch of intermediate functions that don’t matter, resulting in the tissue of the kidney responding one way to the ligand and the tissue of the liver responding a different way. This is an example of what important quality of cell signal transduction?
Microheterogeneity. The same ligand can elicit different (coordinated) responses with a cell, or different cells may respond differently to the same ligand (often due to isozymes*).
What is the most important difference between an agonist and an antagonist?
An agonist initiates a signaling cascade. An antagonist does not, and competitively or noncompetitively inhibit agonists.
List 5 common effector enzymes.
Kinases, lipases, phosphotases, binding facilitators, nucleotidyl cyclases (convert ATP>cAMP or GTP>cGMP).
List 4 common second messengers.
Ip3, Ca+2, DAG, cAMP.
3 important things that must occur for signal to be terminated:
- ) Ligand/receptor complex must be inactivated;
- ) intermediates (effector proteins, second messengers) must be lost (either degraded or diffuse away);
- ) Target protein must return to original state.
Receptor X is a GPCR that binds with hormone Y and triggers a signaling cascade. This cascade activates adenylyl cyclase. A mutation in receptor X causes endogenous molecule Z to covalently bond to the receptor.
Describe molecule Z in terms of its relationship to hormone Y.
What is the result of this mutation?
Molecule Z is an irreversible antagonist.
The result of the mutation is decreased activity of adenylyl cylcase, which converts ATP>cAMP, so low [cAMP] will result (since cAMP activates PKA, reduced PKA activity would also result).
**I made this all up so it might not be realistic, but I wanted a scenario to keep these concepts all straight! :)
In a typical RTK cascade, which protein has GTPase activity?
RAS.
A 65-year-old woman suffering from atrial fibrillation had been taking a drug to treat this condition for 6 months. The drug had no intrinsic activity and bound reversibly to β1 receptors. What term best defines this drug?
Because the drug has no intrinsic activity, we can assume it is an antagonist.
Because it binds reversibly, we know it is a competitor.
Therefore, it can be described as a competitive antagonist.
The thyroid is stimulated to release thyroid hormone by thyroid stimulating hormone (TSH), which is produced by the pituitary gland and transported by the bloodstream. This type of hormonal signaling is called:
Endocrine.
The insulin receptor is a tyrosine kinase receptor. When insulin binds hepatic insulin receptors, a pathway that activates cAMP phosphodiesterase is stimulated. Which of the following events will most likely occur in hepatocytes in response to increased serum insulin levels?
When cAMP phosphodiesterase is stimulated, cAMP will be degraded.
One function of cAMP is to activate PKA, so if [cAMP] is reduced, PKA activity will decrease.
Are the charges on carboxyl, amino, and side chain groups of amino acids universal?
No, they depend on pH of environment.
At physiological pH (7.4), the amino acid is positively charged and the carboxyl group is negatively charged.
What determines the formation of a-helicies and b-sheets?
Backbone interactions (so primary structure). R groups do not affect formation of these structures.
What fundamentally determines protein folding?
Primary structure.
What determines tertiary structure?
The interactions of side chains (ex: electrostatic interactions, Van der Waal’s forces, etc).
